haplo | A nice control panel for HAProxy | Proxy library

I have a development laptop (Mint 19.3), and a test server (Ubuntu 18.04.4 LTS).

The laptop is Docker version 19.03.5, build 633a0ea838, the server is Docker version 19.03.12, build 48a66213fe

I'm running Python 3.6 code inside the container, which uses subprocess (code below) to create an sshfs mount to a third server, after which the python code walks through the mounted directory.

Everything works fine on my development laptop. But on the server, the directory mounts (and is seen with the mount command) however cd'ing into the directory just hangs, and the Python code's subsequent walk just hangs. (NOTE: The python code never crashes or errors out. It just hangs forever.)

HOWEVER, if I manually use the same sshfs command at the container's command line, the directory works fine.

I'm at a loss as to how to troubleshoot this.

===2020-09-25 UPDATE===

OK. Since the Python code uses subprocess, the sshfs mount is obviously available to any terminal windows that wants to use it.

I have tried accessing the mount from a new terminal window inside the container, but when I cd to the mount - the window just freezes.

Well, I left everything sitting overnight - and now when I try to cd into the mount ... it works. It's like the mount has to sit for hours before it will work.

Any ideas?

Python code

I have a data frame that I am working with that is a series of probabilities as output from an HMM. I want to know the number of times that the probability switches from being above an arbitrary critical value to being below that value and vice versa. I am very new to R, and while I developed a code that produces an output, it is rather time intensive.

I downloaded 876 DNA sequences of a 276 nucleotides length and made a df with the information. TOTAL <- read.csv("TOTAL.csv") TOTAL Ind Seq Tipo 1 AACTTTCAACAACGGATCTCTTGGTTC... _NA_ 2 AACTTTTAAAAACGGGTTCTTTGGTTC... _NA_ 3 AACTTTCAACAACGGATCTCTTGGTTC... _NA_ 4 AACTTTCAACAACGGATCTCTTGGTTC... _NA_ 52 AACTTTCAACAACGGATCTCTTGGGTC... _NA_ 821 AACTTTCAACAACGGATTTTTTGGTTC... _NA_ 876 AACTTTCAACAACGGATCTCTTGGTTN... _NA_

I then extracted the uniques sequences, found there are 53 different types of sequences. Finally I assigned to each unique sequence a character value from "A" to "BA". UNIQUE <- read.csv("UNIQUE.csv") UNIQUE Ind Seq Tipo 1 AACTTTCAACAACGGATCTCTTGGTTC... A 2 AACTTTTAAAAACGGGTTCTTTGGTTC... B 3 AACTTTCAACAACGGATCTCTTGGTTC... C 10 AACTTTCAACAACGGATCTCTTGGGTC... J 30 AACTTTCAACAACGGATTTTTTGGTTC... AD 53 AACTTTCAACAACGGATCTCTTGGTTN... BA

What I want is, for every value in TOTAL$Seq find a match in UNIQUE$Seq. Then assign to TOTAL$Haplo a value in UNIQUE$Haplo that corresponds to the matched with UNIQUE$Seq. How can I do that? TOTAL Ind Seq Tipo 1 AACTTTCAACAACGGATCTCTTGGTTC... A 2 AACTTTTAAAAACGGGTTCTTTGGTTC... B 3 AACTTTCAACAACGGATCTCTTGGTTC... C 4 AACTTTCAACAACGGATCTCTTGGTTC... C 52 AACTTTCAACAACGGATCTCTTGGGTC... J 821 AACTTTCAACAACGGATTTTTTGGTTC... AD 876 AACTTTCAACAACGGATCTCTTGGTTN... BA

I am working with "rehh" package of R.

I create an object chr21 of class haplohh from data2haplohh function of the package.

Now when I try to write it to a file: